The Chromosome that Broke the Camel’s Back

I’ve been asked what the tipping point was for me to accept the Theory of Evolution after resisting it for most of my life. As I researched, the weight of the evidence was cumulative, so the fact that flipped the switch for me was more a function of timing and the order I just happened to have discovered things, as opposed to necessarily the strongest or best argument. That said, I do happen to remember what it was.

(Quick aside: I’m aware that millions of people around the world accept science like evolution, geology, cosmology, paleontology and the big bang while at the same time believing in a God. In fact, this is the official position of the Catholic church. This is one reason I will be attempting to keep discussion of science and religion separate on my blog when the topic doesn’t require conflation.)

Humans have 23 pairs of chromosomes, while all the other great apes have 24 pairs. If evolution proposes that apes and humans share a common ancestor, this difference must be explained. It was hypothesized that a mutation fused two of the ape chromosomes creating just one in humans. And that is what modern genetics has found.

In 2005, a paper was published comprehensively identifying where two analogous chromosomes of the non-human great apes fused end-to-end to create human chromosome 2. Our chromosome has end markers (the telomere) in the middle, and two middle-sequences (centromeres) laid out in the pattern that is consistent which such fusing. The first centromere of human chromosome 2 lines up with chimp chromosome 2p, while the second centromere matches chimp 2q.

I’m not a geneticist. The last time I was in a formal biology class, the technology to sequence these genes was a far-off science-fiction dream. So rather than embarrass myself further, I’d point you to this short video that explains the finding much better than I could.

 

This initial finding has been corroborated by significant research in the years since.

If you are feeling curious and ambitious, I would encourage you to dig deeper into the science yourself, as I did. Much of it is over my head, but it was enough to conclusively convince me that our chromosome 2 is a fusion of two common ancestor’s chromosomes. (And amazed me at what has happened in the field of genetics while I was off marketing space movies.) The evidence is difficult to explain by any other mechanism.

I was so convinced, I named this blog after it.

As you research this yourself, you may also find amateur authors attempting to use jargon to paint minor cherry-picked disagreements (some since settled) among geneticists about the “how” this happened as some kind of scientific doubt about the “what” happened. I find this trend unfortunate, as scientists publicly refining the work of other scientists is what gives science its power, not its weakness.

I’m happy for you, Star Wars. I am.

In just a month, Star Wars: The Force Awakens opens in movie theaters.

In October 1999, my life-long fandom and involvement with the popular Star Wars website TheForce.net landed me at a lunch on Skywalker Ranch which lead to my recruitment to take over the efforts at StarWars.com. I picked up my family, moved to the Bay Area, and for seven years was part of Lucasfilm’s marketing team through the remaining Star Wars prequels. I look back at that time as the best professional experience of my life for many reasons, but most of all the sheer uncompromising excellence of every person I had the pleasure of working with.

In 2006, I was burned out, missing my young children, and facing the gauntlet of Indiana Jones 4 with no further Star Wars in sight. I left my position at Lucasfilm to move back to Canada and start new life chapters.

In 2012, it was announced that Disney had purchased Lucasfilm and that a new wave of Star Wars films would be made. From my desk in Calgary, I had decidedly mixed emotions. As a fan, the prospect of a breath of fresh air in my beloved franchise made me giddy. On a professional level, my heart sank. There will be more Star Wars, and I will not be involved.

In the months that followed, many Lucas friends and colleagues ended up losing their jobs as Disney consolidated operations. I consoled myself that, in all likelihood, I would not have kept my position in the new efforts even if I had stayed. That said, a handful of those I worked with closely kept their positions and continue to guide the company and the story. So… maybe I could have done the same? I can talk myself into either possibility, depending how I want to feel about it.

I am proud that there are hints of the legacy of what I was trying to accomplish with the online marketing that have carried forward, even if such hints are in my mind only. I am proud of the team that I fought alongside who are still at Lucasfilm making a difference.

I am sad that the trivial blips I was able to contribute to official Star Wars lore were swept away in the expanded universe reboot… even though I am strongly in support of that housecleaning. (And advocated such a move while at Lucasfilm.)

I worry that the new Star Wars films will be amazing, and my time with Star Wars will be further tainted with some kind of asterisk because I was on board for the bad films.

If I could sum it up best, I feel like the girl who said “see you later” to Avril Lavigne’s Sk8er Boi and now stands in the concert crowd looking up at the guitar-playing Star Wars that I turned down.

That said, I will never be able to experience Attack of the Clones or Revenge of the Sith as a fan. I will think of the scenes I was off camera for. I will remember scene development and behind-the-scenes turmoil. I will remember alternate edits and creative choices. I wouldn’t trade it, but it’s something I can’t experience purely even these years later.

And so, with a month left to The Force Awakens, I’ve decided to make the most of it. I’ve avoided much of the speculation and spoilers. The day-to-day news. I’m avoiding all the new footage in commercials.

When I walk in to the first showing (not even a special screening) in my city on opening night, I will do so as a regular fan. Enjoying my trip to a galaxy far, far away just as the creators intended. Where I began.

Spock was the Worst Wookiee

Most people enjoy lively conversations about topics that they are knowledgable and passionate about. An attentive conversant to whom you’re introducing ideas and experiences can reignite one’s own spark. Finding someone who shares your passion on the same level is invigorating.

The best stimulation can be a person who has a differing, but equally-knowledgeable, take on the subject. I’ll take informed disagreement any time.

But for me, the least enjoyable conversation is with someone who is ill-informed on the fundamentals of a topic, yet speaks authoritatively with misconceptions. Escape or topic change is the only way out. “Toronto is the capital of Canada.” “The director just tells the computer to put dinosaurs in the movie.” “Someone decided who would win this game before the season even started.” “The whole internet was down.” (All things that have been said to me.)

One of my current passions is physical science of all kinds, with the model of biological evolution at the forefront of my curiosity. While I welcome significant conversations about the diversity of life, I have found that many who would like to engage haven’t taken the time to understand the tenets of the claim in order to evaluate it.

10702094_719679078148476_3565313758563080008_nSomeone of significant intellect, whom I admire greatly, linked to this “if the theory of evolution were true” meme image on Facebook last night, affirming its wisdom. I wanted to reply in frustration, but simply couldn’t. The last time I saw so many things wrong in one image, it was an observation game on the back of a cereal box. The Theory of Evolution that is being questioned here, simply doesn’t exist anywhere in science.

While I am nothing more than an enthusiastic student, here are a non-comprehensive handful of statements shared with me recently that indicated that the speaker was mistaken about the claims made by the Unified Theory of Biology (aka Evolution). My brief clarifications are even less comprehensive.

“If we evolved from monkeys, why are there still monkeys?”

It is actually apes with whom humans have a claimed common ancestor, in the same way that cousins share a common grandparent. My children did not cease to exist when my nieces were born. Europe did not cease to exist when the Americas were colonized.

“There are no transitional fossils.”

Every organism that has ever lived was a transitional form between one generation and the next. (Well, individuals that die before reproducing would technically be a node.) Every fossil ever found is a transitional fossil. Whether such transitions are compelling to you is a matter of taste, but they all exist. (Side note… check out the plucky tiktaalik, if you’re not familiar. He’s cool.)

“Evolution is only a theory.”

It is unfortunate that the common use of the word theory conflates it with an unproven guess or uncertain hypothesis. In science, a theory is a set of principles that has repeatedly-proven power to explain and predict a class of observed phenomena. A theory is the highest title a scientific idea can achieve. If it were a Saturday morning cartoon, a scientific law would be sitting on the stairs of a university singing about how it hoped to one day be a theory.

“Evolution can’t add genetic information.”

Mutations demonstrably add, remove or scramble genes. As a terrible analogy, let’s start with CAT. With mutation, we might get ACT, TAC, TACT or AT. Which of those have less information? More?

“A female cat and a male cat just happened to have evolved at the same time and found each other?”

The populations that descend from ancestors who reproduced sexually would contain a mix of sexes.

“You expect me to believe that after enough gusts of wind blow through a junk yard that eventually a fully-equipped 747 will appear?”

Evolution does not predict spontaneous appearance due to chance. It describes the incredibly slow process of natural selection of genes in an reproducing population. Airplanes do not reproduce.

I know it’s a lot of fun to express opinions, and that knowing about things is difficult. I have my own inventory of ill-informed opinions on many topics — soccer, lipstick, disorders, computing platform, the merits of multilingualism, and the Oxford comma, to name a few.

But whether I’d like to agree with, disagree with, affirm or question a claim, it seems reasonable that the only effective way to do any of those is to accurately represent the claim. Otherwise, it’s just me telling you that Spock was the worst Wookiee.

There are countless great resources to learn more about the claims of the Theory of Evolution. One of the clearest introductions is Undeniable by Bill Nye (the science guy). Despite his inability to use twitter in a constructive manner, Richard Dawkins has exceptional skill in communicating complex biology in all his books. The Greatest Show on Earth is a good start.

Cognitive Dissonance and Intellectual Dishonesty

Cognitive dissonance is the mental stress and discomfort that comes from holding two or more contradictory beliefs at the same time. This is not the mere hypocrisy that might come from a career nutritionalist who secretly binges on bacon-covered donuts. This is more akin to poor HAL 9000 whose programmed purpose was to relay accurate information, but simultaneously attempted to obey orders to withhold information from Bowman and the crew.

While I didn’t consider mass murder as a solution to my problem, in 2010 (coincidentally, the year that fictional HAL was restored and healed), I could no longer ignore the decades-old splinter in my brain caused by my fundamentalist Christian views and my brushes with logical and scientific discoveries that seemed to conflict. My life was crumbling on many fronts, so this particular indulgence certainly didn’t seem of timely import, but I couldn’t shake it. It was giving me literal headaches.

And so, I did what any golden Mennonite poster-boy would do… I set out to gather the evidence that the Bible was true, in the spirit of 1 Peter 3:15.

Like the awkwardly-healed leg bones that I shattered in middle school, I had been silently carrying this mind splinter since I was a teen. Never quite right, always there, but rarely affecting my life or consciousness.

This wasn’t my first crisis. I was a fresh-faced teen already on his way to a Doogie Howser software career, taking a brief stop at Canadian Bible College in Regina to double-check God’s life map. Fortunately, my first-term marks were high enough to bypass pesky prerequisite requirements and I was allowed jump straight to senior-level apologetics classes. There my eager-to-be-comforted intellect was wrapped in a warm blanket of authorities, vague notions and the traditions of generations. Cherry-picked interpretations were given to me in a warm mug while thick velvet choir curtains shielded me from outside questions. Google was years away. I left satiated.

My big disconnects were the global flood and creation. I took to Amazon and ordered the best books, and hit my browser for the best websites. Within a week or two, I was sure to have personally inventoried all of the clear evidence for these historical events and I could return my mind to other concerns.

But when I started reading, the evidence wasn’t there. Far worse, what the most renowned minds had written was flimsy. Straw-grasping. Incoherent. Transparently false. I found myself laughing out loud at the scholars I was turning to to save me. The ones who believed what I believed.

And then it came. My beliefs were intellectually dishonest. I had no good reason to believe them. At this point, I had literally nothing to replace them with. I knew nothing of modern cosmology, abiogenesis, geology or evolution.

All I knew what that intellectual dishonesty was worse than cognitive dissonance.

At the time, I was still a leader to hundreds of teens memorizing scripture week-by-week. I had nothing to say to them. I immediately delegated all Bible teaching and all public prayer. This was easy to do under the guise of mentorship, but I couldn’t disrespect them with my unbelief.

I prayed my last public prayer. Lost.

(photo by r. nial bradshaw)

I’m radioactive, radioactive

One week ago tonight, I was preparing myself to check in to the hospital for chemotherapy treatment for a rare cancerous sarcoma.

The process began Monday morning with a 7 a.m. check-in to get a PICC line (peripherally inserted central catheter) inserted. Ultrasound was used to create a hole in a vein in my tricep area, insert a tube and navigate it to my heart for the purpose of more direct drug injection. Not terrible, but not the most fun. Unfortunately, the stabby attempts to weave the tube through my right side were thwarted by the cancer in my armpit (did I mention I have cancer in my armpit now?). So, I got to have the entire procedure a second time through my left side.

Plumbing inserted, I was sent upstairs to receive my first of three bags of chemotherapy medicine that would slowly drip at about 47 ml/hour over the course of the next 72 hours. I was given a hospital gown to wear for the duration, but negotiated just before attachment to keep my black t-shirt instead. Between that and my primary concern of wifi instructions, I began to make my mark as an atypical patient on the unit.

The other patients on my floor rarely left their rooms. I was rarely in my room. I took up residence in one of the lounges with laptop, iPad and phone in tow. I was first discovered there when the IV pole and monitoring system that was now my dance partner began to squeal. Apparently it has a short battery life. The scolding staff let me know that if I was going to make camp, it would have to be near wall outlets. Fortunately, a lifetime of constant scanning for airport power outlets had prepared me.

Each change in IV bags meant what to me looked like full-on Monsters, Inc. hazmat suits for the staff with plastic poncho, big gloves and facial blast shield. While they were content to allow this poison to go straight to my heart, what they were very concerned with was where I would pee. I was assigned a specific toilet and no other toilet in the universe was acceptable. With my urine now containing isotopes of humanity-jeopardizing lethality, there were protocols for splashing and much documentation. Unfortunately, the one effect that the chemo had on me was to destroy my legendary bladder reputation and haul me into my lead-lined lieu about seven times a day. My urine seemed clear, but it did smell like it might be able to power a flux capacitor.

Lights-out on the unit took place at 9:00 p.m., though the staff smiled at me as I sat reading in the lounge as the clock rolled past. Shift change was at 11 p.m. and the sight of me sitting on the floor with an array of electronics sprawled over a coffee table lent amusement and curiosity to the staff. They didn’t have to wake me for meds or vitals and I did my best to make them laugh, so they played along until 3 a.m. each night when my nocturnal nature probably clashed with their night-shift quiet time. The second night, my nurse quietly took away the Starbucks coffee my parents had lovingly delivered to me and replaced it with apple juice. Each new nurse joked about odd notes in my chart about my behavior, but I felt well liked.

On the opposite end of the spectrum was my roommate. He was a 50-something man who did not speak English well. On top of his cancer, he had completely lost his short-term memory. He was constantly confused about where he was and ripped out his tubes, including those with the burning toxic chemo medication. When I finally did get to sleep, he would be crashing nearly hourly and the lights flicked on to deal with one emergency or another. My sleep was the last of anyone’s concern. The man’s brother, sister and father were with him constantly and gave him great care. I’m sorry that he is unaware of this and that he has such a long way to go. He made me feel I was greatly fortunate, as did most of the other patients.

As the last drops of poison dripped from the bag, through the tube, the machine, the other tube and into my heart, I was a considerably weaker man than the one who walked in. I had yet to feel the full force of nausea that was to greet me later at home, but even the long-awaited shower brought me back to only a shadow.

One last thing remained before I could leave the building… my first of ten doses of radiation therapy. Weeks ago, a team hand-crafted for me an apparatus meant to keep my hand still during this process. It has a custom form-fitted base, a fiberglass mesh cage that contours to my splayed fingers and locks down with screws, all topped with a centimeter-thick bee’s wax encasement. This is meant to allow for incredibly precise bursts meant to impact cancer cells and avoid the remaining healthy cells. Perhaps more on this later.

The radiation room looks a like something from an X-Men movie. The metal slab sits in the center of a circular space that allows for the robot appendage to spin and dance through the three-dimensional grid of green laser lights. If from my vantage point I could see it, I’m sure it would be quite impressive. But the awkward position I’m in lets me see only a sad low-tech bookshelf.

So, I quietly sing Weird Al Yankovic’s “The Saga Begins”. Partially because it soothes me, and partially because its 5:30 running time is the duration of each of my radiation treatments once the robot starts spinning.

I returned Friday for a second dose, then collapsed to sleep for 27 straight hours… a week’s worth all at once, for me. The time has been unkind, but this first week of my treatment journey has passed quickly with the thanks of many friends… some new, some old.

If you are to be believed, “I got this.”

With your help.

The “A word” — and why I use it

This is not my deconversion story. I’m sure I will share that, in pieces and over time, as would be fitting. But this is not it.

Instead, this is a simple address to the advice my kind, compassionate and insightful father posed to me on the night I came out as an atheist. “Perhaps you could cool it on the A-word? It scares people.”

Theism is the “belief in a god or gods”. Etymology tells us that adding the prefix “a” negates the meaning. So, atheism is the lack of belief in a god or gods. That’s all. It is not a claim that no gods exist. It is a belief statement only.

Why not identify as agnostic? That’s not so scary. Agnostics don’t eat babies. Or at least as many babies.

A gnostic is one who claims knowledge. About anything. So an agnostic is one who does not claim knowledge. Since so few claim to know with 100% certainty if there is a god, most of the population is agnostic on the matter. Most people are agnostic theists (I don’t know if there’s a god, but I believe there is) or agnostic atheists (I don’t know if there’s a god, and I don’t believe there is).

Agnostic is not a softer form of atheist.

Owning labels changes minds. Slowly. Ever so slowly. But eventually.

I am not convinced of the claim that a god exists. I am an atheist.

You know an atheist. Do I scare you?

(Huge thank you to every atheist ever, of whom this post is completely and utterly derivative.)

Myxoinflammatory Fibroblastic Sarcoma

I was hauling boxes on June 1, 2015, when I noticed that the back of my right hand was sensitive as it would brush against door jams, van walls or packing material. Inspection that night revealed a small white dot near my knuckle. Spending most of my days typing, I know the back of my hand like the back of my hand. This was new, but not concerning.

A few days later and that dot was a bump. A wart, I decided, in my confident inexperience with anything related. I purchased one of those over-the-counter wart-burning ointments, with the instructions telling me to apply twice-per-day for up to nine weeks. In sadist-like adherence, I applied the scalding acid while watching my wart get bigger each day, seemingly feeding off the pain.

By the time San Diego Comic-Con rolled around in July, the bump was the diameter of a dime and the height of a smartphone. There was a gory split in the middle and I wore a Band-Aid® (the actual brand, not conflating the generic term) at all times to avoid scaring children. The acid was making a monster.

Upon returning home, I decided that medical attention was weeks past due… enough time gap to appease the part of my ego that refuses to seek help. After a few hours of waiting room sniffle-chorus, in what would prove to be the start of a theme, the on-shift doctor squinted at my hand in disgust. She couldn’t tell what was happening, but declared it infected. “Stop it!” was her advice, sending me home with a round of antibiotics.

It was during the antibiotics week that the pain started. The spectrum ranged from a dull throb in my hand to brain-overwhelming searing pulses. Like the xenomorphs who hunted Newt, the worst mostly came out at night… mostly.

Several clinic-level visits later, most involving a crowd of openly-baffled “you have to see this” doctors, it was determined that “let’s cut it out” was the sophisticated course of action. Perhaps the topic of a future post will be the get-what-you-pay-for aspects of free Canadian health care, which manifested early with scheduling my surgery-necessary scans two weeks after my scheduled surgery. American-learned persistence got me through.

My plastic surgery was on August 28. After seeing many more serious cases come through during my wait, I decided to try to keep it light for the medical team. With only local freezing, I watched whole procedure. The doctor carefully snipped out a ping-pong-ball sized white mass that had brain-like folds and appearance. He avoided tendons and veins. With the mass removed and the inner workings of my hand exposed, I amused the assisting resident by flexing and unflexing like the Terminator with his arm-flesh removed. Everyone was jovial. There wasn’t quite enough skin left to close the wound, but the skilled doctor made it work somehow. I was to come back in two weeks to have the metal stitches removed.

Two weeks passed.

I was ready to be done this final step into a life with my two-inch (5 cm) scar. But the previously-laughing surgeon walked into the op room a very different man. His steady hands were shaking as he tried to snip the stitches. His voice cracked as he told me that the biopsy came back as a “rare and aggressive cancer”. He did nothing for my confidence as he avoided answering any follow-up questions. Cancer was not in this plastic surgeon’s expertise and he was more afraid of mis-speaking than providing answers. He wouldn’t even name it for me. I don’t remember the drive home, but I remember my single thought opening my front door. “I have cancer.” (The words “rare” and “aggressive” naturally took up shop in my brain.)

The two-week wait for my cancer center consult was excruciating mental torture. Schrödinger’s cancer. Though I had seen it with my own eyes.

Alone in a room with a team of overly-fascinated cancer specialists, I finally got the name of my enemy — Myxoinflammatory Fibroblastic Sarcoma. It is serious, but as long as it stays in my extremities, common treatments are effective in curing this rare disease. It’s only a problem if it recurs or spreads. (Of course, it has since spread, but is avoiding critical systems.)

Yadda yadda a month of near-daily scans, tests, checks, optimistic news, horror stories and display as a medical curiousity.

Tomorrow I begin 72-straight-hours of chemotherapy. After that will be ten days of localized radiation. The purpose of this is to knock down my cancer before surgery. There isn’t much left in my hand to cut, so this strategy is to save as much as they can and keep me typing into my 90’s.

I will lose my hair. That much everyone agrees upon.

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(Peer-reviewed studies show that patients who are aware that they are being prayed for are the group least likely to have a positive outcome. If you feel compelled to pray, please don’t jeopardize me by letting me know.)